I'm not exactly sure on the discrimination laws so I agree consulting a lawyer is a good idea. Do the laws state that you have to modify your training to accomodate him? If so, then I guess you have to let him train. If not, then you have to decide if you want to make an allowance to accomodate him and run the risk of "If you make an allowance for one then you have to make an allowance for all".

Is what we're talking about (normal practice, but pairing with men only) really such an onerous accommodation?

Accommodations for special situations are made all the time. People with bad knees don't do suwari-waza, people don't participate in certain kinds of vigorous training for various reasons (physical condition, youth, or age), people come late or leave early to accommodate their work schedules. Nobody blinks an eye as long as there is some kind of reasonable explanation. Is adhering to your religious beliefs (and these are well established religious beliefs from well established religions) really such an unreasonable explanation?